151
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Shimazaki Y, Yajima T, Takani M, Yamauchi O. Metal complexes involving indole rings: Structures and effects of metal–indole interactions. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2008.04.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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152
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Nakabayashi Y, Tashiro M, Yajima T, Takani M, Tani A, Motoyama T, Odani A, Yamauchi O. Adduct formation between ternary Pt(II)–amino acid–aromatic diimine complexes and flavin mononucleotide and its effect on redox properties. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.03.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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153
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Shimazaki Y, Yajima T, Nakabayashi Y, Naruta Y, Yamauchi O. Synthesis and characterization of platinum(II) complexes of 2N1O-donor ligands with a pendent indole ring. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.01.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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154
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Dharmarajan L, Case CL, Dunten P, Mukhopadhyay B. Tyr235 of human cytosolic phosphoenolpyruvate carboxykinase influences catalysis through an anion-quadrupole interaction with phosphoenolpyruvate carboxylate. FEBS J 2009; 275:5810-9. [PMID: 19021757 DOI: 10.1111/j.1742-4658.2008.06702.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyr235 of GTP-dependent phosphoenolpyruvate (PEP) carboxykinase is a fully invariant residue. The aromatic ring of this residue establishes an energetically favorable weak anion-quadrupole interaction with PEP carboxylate. The role of Tyr235 in catalysis was investigated via kinetic analysis of site-directed mutagenesis-derived variants. The Y235F change lowered the apparent K(m) for PEP by about six-fold, raised the apparent K(m) for Mn(2+) by about 70-fold, and decreased oxaloacetate (OAA)-forming activity by about 10-fold. These effects were due to an enhanced anion-quadrupole interaction between the aromatic side chain at position 235, which now lacked a hydroxyl group, and PEP carboxylate, which probably increased the distance between PEP and Mn(2+) and consequently affected the phosphoryl transfer step and overall catalysis. For the Y235A and Y235S changes, an elimination of the favorable edge-on interaction increased the apparent K(m) for PEP by four- and six-fold, respectively, and the apparent K(m) for Mn(2+) by eight- and six-fold, respectively. The pyruvate kinase-like activity, representing the PEP dephosphorylation step of the OAA-forming reaction, was affected by the substitutions in a similar way to the complete reaction. These observations indicate that the aromatic ring of Tyr235 helps to position PEP in the active site and the hydroxyl group allows an optimal PEP-Mn(2+) distance for efficient phosphoryl transfer and overall catalysis. The Y235A and Y235S changes drastically reduced the PEP-forming and OAA decarboxylase activities, probably due to the elimination of the stabilizing interaction between Tyr235 and the respective products, PEP and pyruvate.
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Affiliation(s)
- Lakshmi Dharmarajan
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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155
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Shishova EY, Di Costanzo L, Emig FA, Ash DE, Christianson DW. Probing the specificity determinants of amino acid recognition by arginase. Biochemistry 2009; 48:121-31. [PMID: 19093830 DOI: 10.1021/bi801911v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the alpha-amino and alpha-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate alpha-carboxylate and T135, (2) a direct hydrogen bond between the substrate alpha-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate alpha-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased K(M) values but have less pronounced effects on catalytic function as reflected by minimal variations of k(cat). As with substrate K(M) values, inhibitor K(d) values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.
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Affiliation(s)
- Ekaterina Y Shishova
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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156
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Abstract
Simple halogen substituents frequently afford key structural features that account for the potency and selectivity of natural products, including antibiotics and hormones. For example, when a single chlorine atom on the antibiotic vancomycin is replaced by hydrogen, the resulting antibacterial activity decreases by up to 70% (HarrisC. M.; KannanR.; KopeckaH.; HarrisT. M.J. Am. Chem. Soc.1985, 107, 6652−6658). This Account analyzes how structure underlies mechanism in halogenases, the molecular machines designed by nature to incorporate halogens into diverse substrates.
Traditional synthetic methods of integrating halogens into complex molecules are often complicated by a lack of specificity and regioselectivity. Nature, however, has developed a variety of elegant mechanisms for halogenating specific substrates with both regio- and stereoselectivity. An improved understanding of the biological routes toward halogenation could lead to the development of novel synthetic methods for the creation of new compounds with enhanced functions. Already, researchers have co-opted a fluorinase from the microorganism Streptomyces cattleya to produce 18F-labeled molecules for use in positron emission tomography (PET) (DengH.; CobbS. L.; GeeA. D.; LockhartA.; MartarelloL.; McGlincheyR. P.; O’HaganD.; OnegaM.Chem. Commun.2006, 652−654). Therefore, the discovery and characterization of naturally occurring enzymatic halogenation mechanisms has become an active area of research. The catalogue of known halogenating enzymes has expanded from the familiar haloperoxidases to include oxygen-dependent enzymes and fluorinases. Recently, the discovery of a nucleophilic halogenase that catalyzes chlorinations has expanded the repertoire of biological halogenation chemistry (DongC.; HuangF.; DengH.; SchaffrathC.; SpencerJ. B.; O’HaganD.; NaismithJ. H.Nature2004, 427, 561−56514765200). Structural characterization has provided a basis toward a mechanistic understanding of the specificity and chemistry of these enzymes. In particular, the latest crystallographic snapshots of active site architecture and halide binding sites have provided key insights into enzyme catalysis. Herein is a summary of the five classes of halogenases, focusing on the three most recently discovered: flavin-dependent halogenases, non-heme iron-dependent halogenases, and nucleophilic halogenases. Further, the potential roles of halide-binding sites in determining halide selectivity are discussed, as well as whether or not binding-site composition is always a seminal factor for selectivity. Expanding our understanding of the basic chemical principles that dictate the activity of the halogenases will advance both biology and chemistry. A thorough mechanistic analysis will elucidate the biological principles that dictate specificity, and the application of those principles to new synthetic techniques will expand the utility of halogenations in small-molecule development.
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157
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Rashidi-Ranjbar P, Vafakish B. A Novel Molecular Cleft Based on Dioxocin Ring, Part I: Synthesis and Conformational Analysis. HETEROCYCLES 2009. [DOI: 10.3987/com-09-11708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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158
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Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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159
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Jennings WB, McCarthy NJP, Kelly P, Malone JF. Topically resolved intramolecular CH-π interactions in phenylalanine derivatives. Org Biomol Chem 2009; 7:5156-62. [DOI: 10.1039/b916021n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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160
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Shimazaki Y, Takani M, Yamauchi O. Metal complexes of amino acids and amino acid side chain groups. Structures and properties. Dalton Trans 2009:7854-69. [PMID: 19771344 DOI: 10.1039/b905871k] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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161
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Kurtoglu M, Lampidis TJ. From delocalized lipophilic cations to hypoxia: blocking tumor cell mitochondrial function leads to therapeutic gain with glycolytic inhibitors. Mol Nutr Food Res 2009; 53:68-75. [PMID: 19072739 PMCID: PMC2928140 DOI: 10.1002/mnfr.200700457] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
An unexpected similarity between cancer and cardiac muscle cells in their sensitivity to anthracyclines and delocalized lipophilic cations (DLC) prompted a series of studies in which it was shown that the positive charge of these compounds is central to their selective accumulation and toxicity in these two distinct cell types. An initial finding to explain this phenomenon was that cancer and cardiac muscle cells exhibit high negative plasma membrane potentials resulting in increased uptake of these agents. However, the p-glycoprotein efflux pump was shown to be another factor underlying differential accumulation of these compounds, since it recognizes positively charged drugs and thereby actively reduces their intracellular concentrations. The delocalized positive charge and lipophilicity of DLCs leads to their retention and inhibition of ATP synthesis in mitochondria. Years later it was realized that cancer cells in the hypoxic portions of solid tumors were similar to those treated with DLCs in relying mainly on anaerobic metabolism for survival and could thus be targeted with a glycolytic inhibitor, 2-deoxy-D-glucose (2-DG). This hypothesis has lead to a Phase I clinical trial in which 2-DG is used to selectively kill the hypoxic tumor cell population which are resistant to standard chemotherapy or radiation.
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Affiliation(s)
- Metin Kurtoglu
- Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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162
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Miller GP. Advances in the interpretation and prediction of CYP2E1 metabolism from a biochemical perspective. Expert Opin Drug Metab Toxicol 2008; 4:1053-64. [PMID: 18680440 DOI: 10.1517/17425255.4.8.1053] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Cytochrome P450 2E1 (CYP2E1) plays a central role in the metabolism and metabolic activation of a large number of small, mostly xenobiotic compounds. These qualities distinguish CYP2E1 from traditional enzymes and pose significant challenges to understanding the role and consequences of CYP2E1-mediated metabolism. OBJECTIVE This review discusses recent advances in kinetic profiling, quantitative structure-activity relationships and structural studies that have furthered the development of tools to interpret and predict CYP2E1 metabolism. METHODS Analysis of kinetic profiles by specific mechanisms produces important parameters describing specificity, stoichiometry and metabolism of molecules. Quantitative structure-activity relationships reveal a more specific basis for molecular recognition by CYP2E1. The corresponding protein structures imparting these interactions are the focus of chemical modifications, site-directed mutagenesis and homology modeling studies. RESULTS Compilation of kinetic profiling for CYP2E1 substrates established the selectivity for small substrates, whose characteristics could be generalized in parameters for hydrophobicity and steric properties as determined by quantitative structure-activity relationships. The possibility of an effector site for monocyclic compounds added an interesting variable to these modeling efforts. Various structural studies identified important residues contributing to binding and catalysis as well as the volume and location of the active site relative to the heme moiety. Pressure and carbon monoxide-binding experiments also demonstrated the inherent conformational flexibility of CYP2E1 that may contribute to rate-limiting steps during catalytic turnover. CONCLUSION Although combinations of these approaches have reinforced important observations, more work is needed to verify findings and seek broader impacts for various interpretative and predictive tools.
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Affiliation(s)
- Grover P Miller
- University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, 4301 W. Markham Street, Slot 516, Little Rock, AR 72205, USA.
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163
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Zheng H, Comeforo K, Gao J. Expanding the Fluorous Arsenal: Tetrafluorinated Phenylalanines for Protein Design. J Am Chem Soc 2008; 131:18-9. [DOI: 10.1021/ja8062309] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong Zheng
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3801
| | - Kristofer Comeforo
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3801
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3801
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164
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Rhodium complexes of 1,3-diaryltriazenes: Usual coordination, N–H bond activation and, N–N and C–N bond cleavage. J Organomet Chem 2008. [DOI: 10.1016/j.jorganchem.2008.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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165
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Singh M. Physicochemical studies of globular proteins-Bovine serum albumin, egg albumin, and lysozyme-In some aqueous iodide salts solutions of IA group and cetyltrimethyl ammonium bromide systems. J Appl Polym Sci 2008. [DOI: 10.1002/app.26733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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166
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Csontos J, Murphy RF, Lovas S. The role of weakly polar and H-bonding interactions in the stabilization of the conformers of FGG, WGG, and YGG: an aqueous phase computational study. Biopolymers 2008; 89:1002-11. [PMID: 18615659 DOI: 10.1002/bip.21049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The energetics of intramolecular interactions on the conformational potential energy surface of the terminally protected N-Ac-Phe-Gly-Gly-NHMe (FGG), N-Ac-Trp-Gly-Gly-NHMe (WGG), and N-Ac-Tyr-Gly-Gly-NHMe (YGG) tripeptides was investigated. To identify the representative conformations, simulated annealing molecular dynamics (MD) and density functional theory (DFT) methods were used. The interaction energies were calculated at the BHandHLYP/aug-cc-pVTZ level of theory. In the global minima, 10%, 31%, and 10% of the stabilization energy come from weakly polar interactions, respectively, in FGG, WGG, and YGG. In the prominent cases 46%, 62%, and 46% of the stabilization energy is from the weakly polar interactions, respectively, in FGG, WGG, and YGG. On average, weakly polar interactions account for 15%, 34%, and 9% of the stabilization energies of the FGG, WGG, and YGG conformers, respectively. Thus, weakly polar interactions can make an important energetic contribution to protein structure and function.
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Affiliation(s)
- József Csontos
- Department of Biomedical Sciences, Creighton University Medical Center, 2500 California Plaza, Omaha, NE 68178, USA
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167
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Xiao H, Edwards TE, Ferré-D'Amaré AR. Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. CHEMISTRY & BIOLOGY 2008; 15:1125-37. [PMID: 18940672 PMCID: PMC2626642 DOI: 10.1016/j.chembiol.2008.09.004] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 08/28/2008] [Accepted: 09/02/2008] [Indexed: 12/19/2022]
Abstract
The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.
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Affiliation(s)
- Hong Xiao
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
| | - Thomas E. Edwards
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
| | - Adrian R. Ferré-D'Amaré
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
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168
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169
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Dutta S, Basuli F, Castineiras A, Peng SM, Lee GH, Bhattacharya S. Variable Coordination Modes of Benzaldehyde Thiosemicarbazones - Synthesis, Structure, and Electrochemical Properties of Some Ruthenium Complexes. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200800547] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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170
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González JA, Zawadzki M, Domanska U. Thermodynamics of mixtures containing polycyclic aromatic hydrocarbons. J Mol Liq 2008. [DOI: 10.1016/j.molliq.2008.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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171
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Sun H, Greathouse DV, Andersen OS, Koeppe RE. The preference of tryptophan for membrane interfaces: insights from N-methylation of tryptophans in gramicidin channels. J Biol Chem 2008; 283:22233-43. [PMID: 18550546 PMCID: PMC2494914 DOI: 10.1074/jbc.m802074200] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 06/03/2008] [Indexed: 11/06/2022] Open
Abstract
To better understand the structural and functional roles of tryptophan at the membrane/water interface in membrane proteins, we examined the structural and functional consequences of Trp --> 1-methyl-tryptophan substitutions in membrane-spanning gramicidin A channels. Gramicidin A channels are miniproteins that are anchored to the interface by four Trps near the C terminus of each subunit in a membrane-spanning dimer. We masked the hydrogen bonding ability of individual or multiple Trps by 1-methylation of the indole ring and examined the structural and functional changes using circular dichroism spectroscopy, size exclusion chromatography, solid state (2)H NMR spectroscopy, and single channel analysis. N-Methylation causes distinct changes in the subunit conformational preference, channel-forming propensity, single channel conductance and lifetime, and average indole ring orientations within the membrane-spanning channels. The extent of the local ring dynamic wobble does not increase, and may decrease slightly, when the indole NH is replaced by the non-hydrogen-bonding and more bulky and hydrophobic N-CH(3) group. The changes in conformational preference, which are associated with a shift in the distribution of the aromatic residues across the bilayer, are similar to those observed previously with Trp --> Phe substitutions. We conclude that indole N-H hydrogen bonding is of major importance for the folding of gramicidin channels. The changes in ion permeability, however, are quite different for Trp --> Phe and Trp --> 1-methyl-tryptophan substitutions, indicating that the indole dipole moment and perhaps also ring size and are important for ion permeation through these channels.
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Affiliation(s)
- Haiyan Sun
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
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172
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Othman R, Kiat TS, Khalid N, Yusof R, Irene Newhouse E, Newhouse JS, Alam M, Rahman NA. Docking of Noncompetitive Inhibitors into Dengue Virus Type 2 Protease: Understanding the Interactions with Allosteric Binding Sites. J Chem Inf Model 2008; 48:1582-91. [DOI: 10.1021/ci700388k] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rozana Othman
- Pharmacy Department and Department of Molecular Medicine, Faculty of Medicine and Institute of Biological Sciences and Chemistry Department, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia, Sunway University College, Bandar Sunway, 46150 Petaling Jaya, Malaysia, Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, Maui High Performance Computing Center, 550 Lipoa Parkway, Kihei, Hawaii 96753
| | - Tan Siew Kiat
- Pharmacy Department and Department of Molecular Medicine, Faculty of Medicine and Institute of Biological Sciences and Chemistry Department, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia, Sunway University College, Bandar Sunway, 46150 Petaling Jaya, Malaysia, Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, Maui High Performance Computing Center, 550 Lipoa Parkway, Kihei, Hawaii 96753
| | - Norzulaani Khalid
- Pharmacy Department and Department of Molecular Medicine, Faculty of Medicine and Institute of Biological Sciences and Chemistry Department, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia, Sunway University College, Bandar Sunway, 46150 Petaling Jaya, Malaysia, Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, Maui High Performance Computing Center, 550 Lipoa Parkway, Kihei, Hawaii 96753
| | - Rohana Yusof
- Pharmacy Department and Department of Molecular Medicine, Faculty of Medicine and Institute of Biological Sciences and Chemistry Department, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia, Sunway University College, Bandar Sunway, 46150 Petaling Jaya, Malaysia, Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, Maui High Performance Computing Center, 550 Lipoa Parkway, Kihei, Hawaii 96753
| | - E. Irene Newhouse
- Pharmacy Department and Department of Molecular Medicine, Faculty of Medicine and Institute of Biological Sciences and Chemistry Department, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia, Sunway University College, Bandar Sunway, 46150 Petaling Jaya, Malaysia, Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, Maui High Performance Computing Center, 550 Lipoa Parkway, Kihei, Hawaii 96753
| | - James S. Newhouse
- Pharmacy Department and Department of Molecular Medicine, Faculty of Medicine and Institute of Biological Sciences and Chemistry Department, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia, Sunway University College, Bandar Sunway, 46150 Petaling Jaya, Malaysia, Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, Maui High Performance Computing Center, 550 Lipoa Parkway, Kihei, Hawaii 96753
| | - Masqudul Alam
- Pharmacy Department and Department of Molecular Medicine, Faculty of Medicine and Institute of Biological Sciences and Chemistry Department, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia, Sunway University College, Bandar Sunway, 46150 Petaling Jaya, Malaysia, Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, Maui High Performance Computing Center, 550 Lipoa Parkway, Kihei, Hawaii 96753
| | - Noorsaadah Abdul Rahman
- Pharmacy Department and Department of Molecular Medicine, Faculty of Medicine and Institute of Biological Sciences and Chemistry Department, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia, Sunway University College, Bandar Sunway, 46150 Petaling Jaya, Malaysia, Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, Maui High Performance Computing Center, 550 Lipoa Parkway, Kihei, Hawaii 96753
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173
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Wan ZL, Huang K, Hu SQ, Whittaker J, Weiss MA. The structure of a mutant insulin uncouples receptor binding from protein allostery. An electrostatic block to the TR transition. J Biol Chem 2008; 283:21198-210. [PMID: 18492668 PMCID: PMC2475698 DOI: 10.1074/jbc.m800235200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 05/01/2008] [Indexed: 11/06/2022] Open
Abstract
The zinc insulin hexamer undergoes allosteric reorganization among three conformational states, designated T(6), T(3)R(3)(f), and R(6). Although the free monomer in solution (the active species) resembles the classical T-state, an R-like conformational change is proposed to occur upon receptor binding. Here, we distinguish between the conformational requirements of receptor binding and the crystallographic TR transition by design of an active variant refractory to such reorganization. Our strategy exploits the contrasting environments of His(B5) in wild-type structures: on the T(6) surface but within an intersubunit crevice in R-containing hexamers. The TR transition is associated with a marked reduction in His(B5) pK(a), in turn predicting that a positive charge at this site would destabilize the R-specific crevice. Remarkably, substitution of His(B5) (conserved among eutherian mammals) by Arg (occasionally observed among other vertebrates) blocks the TR transition, as probed in solution by optical spectroscopy. Similarly, crystallization of Arg(B5)-insulin in the presence of phenol (ordinarily a potent inducer of the TR transition) yields T(6) hexamers rather than R(6) as obtained in control studies of wild-type insulin. The variant structure, determined at a resolution of 1.3A, closely resembles the wild-type T(6) hexamer. Whereas Arg(B5) is exposed on the protein surface, its side chain participates in a solvent-stabilized network of contacts similar to those involving His(B5) in wild-type T-states. The substantial receptor-binding activity of Arg(B5)-insulin (40% relative to wild type) demonstrates that the function of an insulin monomer can be uncoupled from its allosteric reorganization within zinc-stabilized hexamers.
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Affiliation(s)
- Zhu-li Wan
- Departments of Biochemistry
and Nutrition, Case Western Reserve
University School of Medicine, Cleveland, Ohio 44106
| | - Kun Huang
- Departments of Biochemistry
and Nutrition, Case Western Reserve
University School of Medicine, Cleveland, Ohio 44106
| | - Shi-Quan Hu
- Departments of Biochemistry
and Nutrition, Case Western Reserve
University School of Medicine, Cleveland, Ohio 44106
| | - Jonathan Whittaker
- Departments of Biochemistry
and Nutrition, Case Western Reserve
University School of Medicine, Cleveland, Ohio 44106
| | - Michael A. Weiss
- Departments of Biochemistry
and Nutrition, Case Western Reserve
University School of Medicine, Cleveland, Ohio 44106
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175
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Goeminne A, Berg M, McNaughton M, Bal G, Surpateanu G, Van der Veken P, De Prol S, Versées W, Steyaert J, Haemers A, Augustyns K. N-Arylmethyl substituted iminoribitol derivatives as inhibitors of a purine specific nucleoside hydrolase. Bioorg Med Chem 2008; 16:6752-63. [PMID: 18571422 DOI: 10.1016/j.bmc.2008.05.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 05/21/2008] [Accepted: 05/28/2008] [Indexed: 10/22/2022]
Abstract
A key enzyme within the purine salvage pathway of parasites, nucleoside hydrolase, is proposed as a good target for new antiparasitic drugs. We have developed N-arylmethyl-iminoribitol derivatives as a novel class of inhibitors against a purine specific nucleoside hydrolase from Trypanosoma vivax. Several of our inhibitors exhibited low nanomolar activity, with 1,4-dideoxy-1,4-imino-N-(8-quinolinyl)methyl-d-ribitol (UAMC-00115, K(i) 10.8nM), N-(9-deaza-adenin-9-yl)methyl-1,4-dideoxy-1,4-imino-d-ribitol (K(i) 4.1nM), and N-(9-deazahypoxanthin-9-yl)methyl-1,4-dideoxy-1,4-imino-d-ribitol (K(i) 4.4nM) being the three most active compounds. Docking studies of the most active inhibitors revealed several important interactions with the enzyme. Among these interactions are aromatic stacking of the nucleobase mimic with two Trp-residues, and hydrogen bonds between the hydroxyl groups of the inhibitors and amino acid residues in the active site. During the course of these docking studies we also identified a strong interaction between the Asp40 residue from the enzyme and the inhibitor. This is an interaction which has not previously been considered as being important.
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Affiliation(s)
- Annelies Goeminne
- Department of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, Antwerp B-2610, Belgium
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176
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Xiao H, Murakami H, Suga H, Ferré-D'Amaré AR. Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 2008; 454:358-61. [PMID: 18548004 DOI: 10.1038/nature07033] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Accepted: 04/28/2008] [Indexed: 11/09/2022]
Abstract
In modern organisms, protein enzymes are solely responsible for the aminoacylation of transfer RNA. However, the evolution of protein synthesis in the RNA world required RNAs capable of catalysing this reaction. Ribozymes that aminoacylate RNA by using activated amino acids have been discovered through selection in vitro. Flexizyme is a 45-nucleotide ribozyme capable of charging tRNA in trans with various activated l-phenylalanine derivatives. In addition to a more than 10(5) rate enhancement and more than 10(4)-fold discrimination against some non-cognate amino acids, this ribozyme achieves good regioselectivity: of all the hydroxyl groups of a tRNA, it exclusively aminoacylates the terminal 3'-OH. Here we report the 2.8-A resolution structure of flexizyme fused to a substrate RNA. Together with randomization of ribozyme core residues and reselection, this structure shows that very few nucleotides are needed for the aminoacylation of specific tRNAs. Although it primarily recognizes tRNA through base-pairing with the CCA terminus of the tRNA molecule, flexizyme makes numerous local interactions to position the acceptor end of tRNA precisely. A comparison of two crystallographically independent flexizyme conformations, only one of which appears capable of binding activated phenylalanine, suggests that this ribozyme may achieve enhanced specificity by coupling active-site folding to tRNA docking. Such a mechanism would be reminiscent of the mutually induced fit of tRNA and protein employed by some aminoacyl-tRNA synthetases to increase specificity.
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Affiliation(s)
- Hong Xiao
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
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177
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Csontos J, Palermo NY, Murphy RF, Lovas S. Calculation of weakly polar interaction energies in polypeptides using density functional and local Møller-Plesset perturbation theory. J Comput Chem 2008; 29:1344-52. [PMID: 18172837 DOI: 10.1002/jcc.20898] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The interaction energies of ubiquitous weakly polar interactions in proteins are comparable with those of hydrogen bonds, consequently, they stabilize local, secondary, and tertiary structures. However, the most widely-used density functionals fail to describe the weakly polar interactions. Thus, it is important to find and test functionals which adequately describe and quantify the energetics of such interactions. For this purpose, interaction energies in the hydrophobic core of rubredoxin (PDB id: 1rb9) and in the S22 subset of the JSCH-2005 benchmark database were computed with the BHandHLYP and PWPW91 functionals and with the pseudospectral implementation of the local MP2 (PS-LMP2) method. The cc-pVDZ, cc-pVTZ(-f), cc-pVTZ, cc-pVQZ(-g), aug-cc-pVDZ, aug-cc-VTZ(-f), and aug-cc-pVTZ basis sets were used for the calculations. In the S22 subset the PS-LMP2 results were extrapolated to the complete basis set limit. Furthermore, the a posteriori counterpoise method of Boys and Bernardi was used to correct the basis set superposition errors in the calculation of interaction energies. Calculations using the BHandHLYP functional, both for the various weakly polar interactions in rubredoxin and for the dispersion interactions in the S22 subset, were in good agreement with those using the coupled cluster (CCSD(T)) and the resolution of identity MP2 (RIMP2) methods and clearly outperformed both the PWPW91 functional and the PS-LMP2 method. The results for the S22 hydrogen bonded subset, obtained with PWPW91 calculations, were closest to those of the reference high level calculations. For the "mixed" (hydrogen bonded and dispersive) interactions in the S22 subset, results obtained with the BHandHLYP and PS-LMP2 calculations agreed well with the reference calculations.
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Affiliation(s)
- József Csontos
- Department of Biomedical Sciences, Creighton University Medical Center, 2500 California Plaza, Omaha, Nebraska 68178, USA
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178
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Solvothermal Synthesis, Crystal Structure and DNA Binding Studies of a 3D Supramolecular Complex {[Cu(phen)CN][Cu(phen)][Cu(CN)2]} n Assembled by Double Curvy Chains. J Inorg Organomet Polym Mater 2008. [DOI: 10.1007/s10904-008-9211-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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179
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Yamauchi O, Yajima T, Fujii R, Shimazaki Y, Yabusaki M, Takani M, Tashiro M, Motoyama T, Kakuto M, Nakabayashi Y. CH⋯Metal(II) axial interaction in planar complexes (metal=Cu, Pd) and implications for possible environmental effects of alkyl groups at biological copper sites. J Inorg Biochem 2008; 102:1218-26. [DOI: 10.1016/j.jinorgbio.2007.11.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 10/15/2007] [Accepted: 11/30/2007] [Indexed: 11/29/2022]
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180
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Faure G, Bornot A, de Brevern AG. Protein contacts, inter-residue interactions and side-chain modelling. Biochimie 2008; 90:626-39. [DOI: 10.1016/j.biochi.2007.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 11/22/2007] [Indexed: 10/22/2022]
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181
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Hatfield MPD, Palermo NY, Csontos J, Murphy RF, Lovas S. Quantum chemical quantification of weakly polar interaction energies in the TC5b miniprotein. J Phys Chem B 2008; 112:3503-8. [PMID: 18303883 DOI: 10.1021/jp077674h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tertiary structure of the TC5b miniprotein is stabilized by inter-residue interactions of the Trp-cage, which is composed of a Tyr and several Pro residues surrounding a central Trp residue. The interactions include Ar-Ar (aromatic side-chain-aromatic side-chain), Ar-NH (aromatic side-chain-backbone amide), and CH-pi (aromatic side-chain-aliphatic hydrogen) interactions. In the present work, the strength of the weakly polar interactions found in the TC5b miniprotein was quantified using all of the available 38 NMR structures (1L2Y) from the Protein Data Bank with DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory and molecular fragmentation with capping of the partial structures. The energies of interaction between the individual residues of the Trp-cage range between -5.85+/-1.41 and -21.30+/-0.88 kcal mol(-1), leading to a significant total structural stabilization energy of -52.13+/-2.56 kcal mol(-1) of which about 50% is from the weakly polar interactions. Furthermore, the strengths of the individual weakly polar interactions are between -2.32+/-0.17 and -2.93+/-0.12 kcal mol(-1) for the CH-pi interactions, between -2.48+/-0.97 and -3.09+/-1.02 kcal mol(-1) for the Ar-NH interaction and -2.74+/-1.06 kcal mol(-1) for the Ar-Ar interaction.
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182
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Xie J, Liu W, Schultz PG. A genetically encoded bidentate, metal-binding amino acid. Angew Chem Int Ed Engl 2008; 46:9239-42. [PMID: 17893898 DOI: 10.1002/anie.200703397] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jianming Xie
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA
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183
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Palermo NY, Csontos J, Murphy RF, Lovas S. The Role of Aromatic Residues in Stabilizing the Secondary and Tertiary Structure of Avian Pancreatic Polypeptide. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2008; 108:814-819. [PMID: 18985166 PMCID: PMC2577375 DOI: 10.1002/qua.21521] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Avian Pancreatic Polypeptide is a 36 residue protein that exhibits a tertiary fold. Results of previous experimental and computational studies indicate that the structure of aPP is stabilized more by non-bonded interactions than by the hydrophobic effect. Aromatic residues are known to participate in a variety of long range non-bonded interactions, with both backbone atoms and the atoms of other side-chains, which could be responsible, in part, for the stability of both the local secondary structure and the tertiary fold. The effect of these aromatic interactions on the stability of aPP was calculated using BHandHLYP/cc-pVTZ. Aromatic residues were shown to participate in multiple hydrogen bonded and weakly polar interactions in the secondary structure. The energies of the weakly polar interactions are comparable with those of hydrogen bonds. Aromatic residues were also shown to participate in multiple weakly polar interactions across the tertiary fold, again with energies similar to those of hydrogen bonds.
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Affiliation(s)
- Nicholas Y Palermo
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
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184
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Dasgupta M, Nag S, Das G, Nethaji M, Bhattacharya S. N,N′-Bis(aryl)pyridine-2,6-dicarboxamide complexes of ruthenium: Synthesis, structure and redox properties. Polyhedron 2008. [DOI: 10.1016/j.poly.2007.08.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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185
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Halder S, Peng SM, Lee GH, Chatterjee T, Mukherjee A, Dutta S, Sanyal U, Bhattacharya S. Synthesis, structure, spectroscopic properties and cytotoxic effect of some thiosemicarbazone complexes of palladium. NEW J CHEM 2008. [DOI: 10.1039/b707448d] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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186
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Rowe GE, Aomari H, Chevaldina T, Lafrance M, St-Arnaud S. Thermodynamics of hydrophobic interaction chromatography of acetyl amino acid methyl esters. J Chromatogr A 2008; 1177:243-53. [DOI: 10.1016/j.chroma.2007.09.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 09/10/2007] [Accepted: 09/13/2007] [Indexed: 11/24/2022]
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187
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Grealis JP, Müller-Bunz H, Ortin Y, Condell M, Casey M, McGlinchey MJ. Birch reduction of hexaphenyl- and pentaphenylbenzene and an X-ray crystallography and NMR spectroscopy study of cis- and epi-1,2,3,4,5,6-hexaphenylcyclohexane and of 2,3,5,6-tetraphenyl-1,1'-bicyclohexylidene: Cannizzaro's conundrum revisited. Chemistry 2007; 14:1552-60. [PMID: 18092316 DOI: 10.1002/chem.200701306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The Birch reduction of hexaphenylbenzene yields two isomers of 1,2,3,4,5,6-hexaphenylcyclohexane. The X-ray crystal structure of the all-cis isomer, 1, reveals that the severe steric crowding among the three axial phenyls is alleviated by a marked splaying out of those three aryl substituents relative to the positioning in a conventional chair structure. A second product, 2, was identified crystallographically and by NMR spectroscopy as the 1,3-diaxial-2,4,5,6-tetraequatorial (epi) isomer of hexaphenylcyclohexane, in which only five of the six additional hydrogen atoms are positioned on the same face of the C(6)Ph(6) precursor. A variable-temperature NMR study of the all-cis isomer 1 yielded a chair-to-chair inversion barrier of approximately 19 kcal mol(-1), which is somewhat higher than the previously reported values for all-cis-1,2,3,4,5,6-C(6)H(6)R(6) in which R=Me or CO(2)Me. The possible relevance to Cannizzaro's 1854 report of a product with the formula (C(7)H(6))(n) is discussed. By contrast, Birch reduction of pentaphenylbenzene led to the formation of 2,3,5,6-tetraphenyl-1,1'-bicyclohexylidene.
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Affiliation(s)
- John P Grealis
- School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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188
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Xie J, Liu W, Schultz P. A Genetically Encoded Bidentate, Metal-Binding Amino Acid. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200703397] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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189
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Collom SL, Laddusaw RM, Burch AM, Kuzmic P, Perry MD, Miller GP. CYP2E1 substrate inhibition. Mechanistic interpretation through an effector site for monocyclic compounds. J Biol Chem 2007; 283:3487-3496. [PMID: 18056994 DOI: 10.1074/jbc.m707630200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In this study we offer a mechanistic interpretation of the previously known but unexplained substrate inhibition observed for CYP2E1. At low substrate concentrations, p-nitrophenol (pNP) was rapidly turned over (47 min(-1)) with relatively low K(m) (24 microM); nevertheless, at concentrations of >100 microM, the rate of pNP oxidation gradually decreased as a second molecule bound to CYP2E1 through an effector site (K(ss) = 260 microm), which inhibited activity at the catalytic site. 4-Methylpyrazole (4MP) was a potent inhibitor for both sites through a mixed inhibition mechanism. The K(i) for the catalytic site was 2.0 microM. Although we were unable to discriminate whether an EIS or ESI complex formed, the respective inhibition constants were far lower than K(ss). Bicyclic indazole (IND) inhibited catalysis through a single CYP2E1 site (K(i) = 0.12 microM). Similarly, 4MP and IND yielded type II binding spectra that reflected the association of either two 4MP or one IND molecule(s) to CYP2E1, respectively. Based on computational docking studies with a homology model for CYP2E1, the two sites for monocyclic molecules, pNP and 4MP, exist within a narrow channel connecting the active site to the surface of the enzyme. Because of the presence of the heme iron, one site supports catalysis, whereas the other more distal effector site binds molecules that can influence the binding orientation and egress of molecules for the catalytic site. Although IND did not bind these sites simultaneously, the presence of IND at the catalytic site blocked binding at the effector site.
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Affiliation(s)
- Samuel L Collom
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Ryan M Laddusaw
- Department of Chemistry, Ouachita Baptist University, Arkadelphia, Arkansas 71998
| | - Amber M Burch
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | | | - Martin D Perry
- Department of Chemistry, Ouachita Baptist University, Arkadelphia, Arkansas 71998
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205.
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190
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Gokel GW. Indole, the aromatic element of tryptophan, as a pi-donor and amphiphilic headgroup. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.ics.2007.07.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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191
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Lee L, Kreutter KD, Pan W, Crysler C, Spurlino J, Player MR, Tomczuk B, Lu T. 2-(2-Chloro-6-fluorophenyl)acetamides as potent thrombin inhibitors. Bioorg Med Chem Lett 2007; 17:6266-9. [PMID: 17889527 DOI: 10.1016/j.bmcl.2007.09.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 08/30/2007] [Accepted: 09/04/2007] [Indexed: 12/01/2022]
Abstract
2-(2-Chloro-6-fluorophenyl)acetamides having 2,2-difluoro-2-aryl/heteroaryl-ethylamine P3 and oxyguanidine P1 substituents are potent thrombin inhibitors (K(i)=0.9-33.9 nM). 2-(5-Chloro-pyridin-2-yl)-2,2-difluoroethylamine was the best P3 substituent, yielding the most potent inhibitor (K(i)=0.7 nM). Replacing the P3 heteroaryl group with a phenyl ring or replacing the difluoro substitution with dimethyl or cyclopropyl groups in the linker reduced the affinity for thrombin significantly. The aminopyridine P1s also provided an increase in potency.
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Affiliation(s)
- Lily Lee
- Drug Discovery, Johnson & Johnson, Pharmaceutical Research and Development, Spring House, PA, USA
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192
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Rana S, Kundu B, Durani S. A mixed-α,β miniprotein stereochemically reprogrammed to high-binding affinity for acetylcholine. Biopolymers 2007; 87:231-43. [PMID: 17879332 DOI: 10.1002/bip.20829] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The protein-structure space is limited to L configuration in the asymmetric alpha-amino acid structures; the function space, on other hand, seems limitless because of the chemical diversity in the amino acid side chain structures. The chemical diversity in side chain structure may be multiplied beneficially with the stereochemical diversity in main chain structure; thus, de novo protein design may be explored for customizing molecular structures stereochemically and molecular functions chemically. Illustrating de novo design in the structure space of L and D alphabet, canonical all-beta folds of poly-L structure were reprogrammed as bracelet, boat, and canoe-shaped molecules-the "boat" as a receptor-like pocket and the "canoe" as a metal-ion receptor-simply by mutating specific L-amino acid residues to the corresponding D stereochemical structure. Demonstrating customization of molecular shape stereochemically and function chemically, a 15-residue mixed-alpha, beta miniprotein of canonical poly-L structure is now reprogrammed stereochemically as a cup-shaped receptor for acetylcholine via cation-pi interaction with a triad of aromatic side chains placed in mimicry of the acetylcholine-receptor sites both natural and artificial. Evidence from CD, fluorescence, NMR, DSC, ITC, MD, and molecular-docking studies is presented to show that a rationally designed 15-residue mixed-L, D peptide is a cooperatively ordered molecular fold in the stereochemically specified molecular morphology, submicromolar in affinity of acetylcholine and thus an acetylcholine receptor exceptionally small and simple. .
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Affiliation(s)
- Soumendra Rana
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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193
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Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 2007; 14:1025-1040. [PMID: 17984965 PMCID: PMC4691843 DOI: 10.1038/nsmb1338] [Citation(s) in RCA: 1091] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Histones comprise the major protein component of chromatin, the scaffold in which the eukaryotic genome is packaged, and are subject to many types of post-translational modifications (PTMs), especially on their flexible tails. These modifications may constitute a 'histone code' and could be used to manage epigenetic information that helps extend the genetic message beyond DNA sequences. This proposed code, read in part by histone PTM-binding 'effector' modules and their associated complexes, is predicted to define unique functional states of chromatin and/or regulate various chromatin-templated processes. A wealth of structural and functional data show how chromatin effector modules target their cognate covalent histone modifications. Here we summarize key features in molecular recognition of histone PTMs by a diverse family of 'reader pockets', highlighting specific readout mechanisms for individual marks, common themes and insights into the downstream functional consequences of the interactions. Changes in these interactions may have far-reaching implications for human biology and disease, notably cancer.
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Affiliation(s)
- Sean D Taverna
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | - Haitao Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | - Alexander J Ruthenburg
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | - C David Allis
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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194
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Huang K, Chan SJ, Hua QX, Chu YC, Wang RY, Klaproth B, Jia W, Whittaker J, De Meyts P, Nakagawa SH, Steiner DF, Katsoyannis PG, Weiss MA. The A-chain of Insulin Contacts the Insert Domain of the Insulin Receptor. J Biol Chem 2007; 282:35337-49. [PMID: 17884811 DOI: 10.1074/jbc.m705996200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The contribution of the insulin A-chain to receptor binding is investigated by photo-cross-linking and nonstandard mutagenesis. Studies focus on the role of Val(A3), which projects within a crevice between the A- and B-chains. Engineered receptor alpha-subunits containing specific protease sites ("midi-receptors") are employed to map the site of photo-cross-linking by an analog containing a photoactivable A3 side chain (para-azido-Phe (Pap)). The probe cross-links to a C-terminal peptide (residues 703-719 of the receptor A isoform, KTFEDYLHNVVFVPRPS) containing side chains critical for hormone binding (underlined); the corresponding segment of the holoreceptor was shown previously to cross-link to a Pap(B25)-insulin analog. Because Pap is larger than Val and so may protrude beyond the A3-associated crevice, we investigated analogs containing A3 substitutions comparable in size to Val as follows: Thr, allo-Thr, and alpha-aminobutyric acid (Aba). Substitutions were introduced within an engineered monomer. Whereas previous studies of smaller substitutions (Gly(A3) and Ser(A3)) encountered nonlocal conformational perturbations, NMR structures of the present analogs are similar to wild-type insulin; the variant side chains are accommodated within a native-like crevice with minimal distortion. Receptor binding activities of Aba(A3) and allo-Thr(A3) analogs are reduced at least 10-fold; the activity of Thr(A3)-DKP-insulin is reduced 5-fold. The hormone-receptor interface is presumably destabilized either by a packing defect (Aba(A3)) or by altered polarity (allo-Thr(A3) and Thr(A3)). Our results provide evidence that Val(A3), a site of mutation causing diabetes mellitus, contacts the insert domain-derived tail of the alpha-subunit in a hormone-receptor complex.
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Affiliation(s)
- Kun Huang
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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195
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Baksi S, Acharyya R, Basuli F, Peng SM, Lee GH, Nethaji M, Bhattacharya S. Rhodium-Mediated C–C Bond Activation of 2-(2′,6′-Dialkylarylazo)-4-methylphenols. Elimination and Migration of Alkyl Groups. Organometallics 2007. [DOI: 10.1021/om700826t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suparna Baksi
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700 032, India, Department of Chemistry, National Taiwan University, Taipei, Taiwan, Republic of China, and Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Rama Acharyya
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700 032, India, Department of Chemistry, National Taiwan University, Taipei, Taiwan, Republic of China, and Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Falguni Basuli
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700 032, India, Department of Chemistry, National Taiwan University, Taipei, Taiwan, Republic of China, and Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Shie-Ming Peng
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700 032, India, Department of Chemistry, National Taiwan University, Taipei, Taiwan, Republic of China, and Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Gene-Hsiang Lee
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700 032, India, Department of Chemistry, National Taiwan University, Taipei, Taiwan, Republic of China, and Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Munirathinam Nethaji
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700 032, India, Department of Chemistry, National Taiwan University, Taipei, Taiwan, Republic of China, and Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Samaresh Bhattacharya
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700 032, India, Department of Chemistry, National Taiwan University, Taipei, Taiwan, Republic of China, and Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
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196
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Affiliation(s)
- Soumya Mitra
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Srinivas Reddy Gurrala
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Robert S. Coleman
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
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197
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Kelkar DA, Chattopadhyay A. The gramicidin ion channel: A model membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2011-25. [PMID: 17572379 DOI: 10.1016/j.bbamem.2007.05.011] [Citation(s) in RCA: 264] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 05/09/2007] [Accepted: 05/10/2007] [Indexed: 02/07/2023]
Abstract
The linear peptide gramicidin forms prototypical ion channels specific for monovalent cations and has been extensively used to study the organization, dynamics and function of membrane-spanning channels. In recent times, the availability of crystal structures of complex ion channels has challenged the role of gramicidin as a model membrane protein and ion channel. This review focuses on the suitability of gramicidin as a model membrane protein in general, and the information gained from gramicidin to understand lipid-protein interactions in particular. Special emphasis is given to the role and orientation of tryptophan residues in channel structure and function and recent spectroscopic approaches that have highlighted the organization and dynamics of the channel in membrane and membrane-mimetic media.
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Affiliation(s)
- Devaki A Kelkar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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198
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Stojanović SD, Medaković VB, Predović G, Beljanski M, Zarić SD. XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. J Biol Inorg Chem 2007; 12:1063-71. [PMID: 17659366 DOI: 10.1007/s00775-007-0276-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 06/28/2007] [Indexed: 11/29/2022]
Abstract
Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that the pi system of every porphyrin ring is involved in XH/pi interactions, with most of the porphyrins having several interactions. Both five-membered pyrrole rings and six-membered chelate rings are involved in XH/pi interactions; the number of interactions with five-membered rings is larger than the number of interactions with six-membered rings. We found interactions with C-H and N-H groups as hydrogen-atom donors; however, the number of CH/pi interactions is much larger than the number of NH/pi interactions. The amino acids involved in the interactions show a high conservation score. Our results that every porphyrin is involved in XH/pi interactions and that amino acids involved in these interactions are highly conserved demonstrate that XH/pi interactions play an important role in porphyrin-protein stability.
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Affiliation(s)
- Srdan D Stojanović
- Department of Chemistry, University of Belgrade, Studentski trg 16, 11001 Belgrade, Serbia
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199
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Minimizing frustration by folding in an aqueous environment. Arch Biochem Biophys 2007; 469:118-31. [PMID: 17719000 DOI: 10.1016/j.abb.2007.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 07/08/2007] [Indexed: 10/23/2022]
Abstract
Although life as we know it evolved in an aqueous medium, the properties of water are not completely understood. In this review, we focus on the role of water in guiding protein folding and stability. Specifically, we discuss the mechanisms of protein folding in an aqueous environment, the effects of water on the folding energy landscape as well as the transition state ensemble, and interactions of water with the folded state. We show that water cannot be viewed as a passive solvent, but rather, plays a very active role in the life of a protein.
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200
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Lee MJ, Huang H, Lin W, Yang RR, Liu CL, Huang CY. Activation of Helicobacter pylori inorganic pyrophosphatase and the importance of Cys16 in thermostability, enzyme activation and quaternary structure. Arch Microbiol 2007; 188:473-82. [PMID: 17598086 DOI: 10.1007/s00203-007-0267-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Revised: 05/16/2007] [Accepted: 05/24/2007] [Indexed: 10/23/2022]
Abstract
The inorganic pyrophosphatase from the human pathogen Helicobacter pylori (HpPPase) is a family I PPase. It is a homohexamer consisting of identical 20-kDa subunits. Hydrolysis of inorganic pyrophosphate (PP(i)) by HpPPase relied on the presence of magnesium and followed Michaelis-Menten kinetics, with k (cat) being 344 s(-1) and K (m) being 83 microM at pH 8.0, which was the optimal pH for catalysis. HpPPase was activated by both thiol and non-thiol reductants, distinct from the previously suggested inactivation/reactivation process involving formation and breakage of disulfide bonds. Substitution of Cys16 of HpPPase, which was neither located at the active site nor evolutionarily conserved, resulted in a loss of 50% activity and a reduction in sensitivity to reductants and oxidized glutathione. In addition, the C16S replacement caused a considerable disruption in thermostability, which exceeded that resulted from active-site mutations such as Y140F HpPPase and those of Escherichia coli. Although Cys16 was not located at the subunit interface of the hexameric HpPPase, sedimentation analysis results suggested that the C16S substitution destabilized HpPPase through impairing trimer-trimer interactions. This study provided the first evidences that the single cysteine residue of HpPPase was involved in enzyme activation, thermostability, and stabilization of quaternary structure.
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Affiliation(s)
- Mon-Juan Lee
- Institute of Biotechnology, National Tsing Hua University, 101, Section 2, Kuang Fu Road, Hsinchu, 30013, Taiwan
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